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Crystal structure of danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with 4-iodo-saha
Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 1 (CD1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WYQ
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 6
- UniProt
- F8W4B7
- Ligands
- UFJ, K, ZN
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 6 | protein | 355 | 44% helix, 14% strand | F8W4B7 |
| B | Histone deacetylase 6 | protein | 354 | 45% helix, 13% strand | F8W4B7 |
Ligands and binding sites
- UFJ · N~1~-hydroxy-N~8~-(4-iodophenyl)octanediamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.79 | 0.81 | 103 | UFJ |
Interfaces
1 interface between chains.
- A–B · 374 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6WYQ · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F8W4B7
- Elsewhere: RCSB PDB 6WYQ · PDBe 6WYQ · UniProt F8W4B7
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